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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ), 'gf_id' => 'HOM05D001298', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001298' ), 'data_identifier' => 'HOM05D001298', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001298', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13430' => 'bna', 'A04p06550' => 'bna', 'A05p41950' => 'bna', 'A07p33050' => 'bna', 'A09p29480' => 'bna', 'A09p46040' => 'bna', 'Aa31LG10G8170' => 'aar', 'Aa31LG5G16540' => 'aar', 'Aa31LG9G15830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3611' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1613' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.629' => 'aag', 'Actinidia10404' => 'ach', 'Actinidia15337' => 'ach', 'Actinidia20393' => 'ach', 'Actinidia21688' => 'ach', 'Actinidia31295' => 'ach', 'Actinidia32460' => 'ach', 'Actinidia32461' => 'ach', 'Actinidia32720' => 'ach', 'Actinidia40157' => 'ach', 'Ah.01g005580' => 'amhyb', 'Ah.08g211010' => 'amhyb', 'Ah.09g228400' => 'amhyb', 'Ah.10g031840' => 'amhyb', 'AL2G23560' => 'aly', 'AL2G23570' => 'aly', 'AL3G16890' => 'aly', 'AL5G33770' => 'aly', 'AL831U10010' => 'aly', 'Aqoxy1G00954' => 'aox', 'Aqoxy2G01457' => 'aox', 'Aqoxy2G03300' => 'aox', 'Aqoxy7G01568' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2N9FFP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HS8E4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJN7R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G7S5MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QS5V0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW40KZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3J4NJ' => 'arhy', 'AT1G60740' => 'ath', 'AT1G65970' => 'ath', 'AT1G65980' => 'ath', 'AT3G06050' => 'ath', 'AT3G52960' => 'ath', 'ATR0315G033' => 'atr', 'ATR0315G058' => 'atr', 'ATR0626G353' => 'atr', 'ATR0820G018' => 'atr', 'Atru.chr4.2534' => 'acertr', 'Atru.chr7.1377' => 'acertr', 'Atru.chr8.1647' => 'acertr', 'AUR62011681' => 'cqu', 'AUR62016506' => 'cqu', 'AUR62033591' => 'cqu', 'AUR62037884' => 'cqu', 'AUR62038066' => 'cqu', 'AUR62038194' => 'cqu', 'BcaB01g00321' => 'bca', 'BcaB01g01417' => 'bca', 'BcaB01g01972' => 'bca', 'BcaB03g15302' => 'bca', 'BcaB05g24147' => 'bca', 'BcaC02g09200' => 'bca', 'BcaC03g14728' => 'bca', 'BcaC04g20949' => 'bca', 'BcaC04g23992' => 'bca', 'BcaC05g30062' => 'bca', 'BcaC07g39660' => 'bca', 'BcaC08g46087' => 'bca', 'BolC2t08307H' => 'bol', 'BolC4t25571H' => 'bol', 'BolC5t34780H' => 'bol', 'BolC6t39024H' => 'bol', 'BolC8t50438H' => 'bol', 'BolC9t56591H' => 'bol', 'BraA02t06401Z' => 'bra', 'BraA04t16357Z' => 'bra', 'BraA04t16359Z' => 'bra', 'BraA05t22917Z' => 'bra', 'BraA07t30933Z' => 'bra', 'BraA09t38514Z' => 'bra', 'BraA09t40067Z' => 'bra', 'C02p21730' => 'bna', 'C04p39990' => 'bna', 'C05p61200' => 'bna', 'C06p39310' => 'bna', 'C08p28270' => 'bna', 'C08p28280' => 'bna', 'C09p37600' => 'bna', 'CAN.G100.70' => 'can', 'CAN.G1138.8' => 'can', 'CAN.G143.22' => 'can', 'CAN.G69.21' => 'can', 'CANSAT02G0002' => 'cansat', 'CANSAT25G3626' => 'cansat', 'CANSAT78G0642' => 'cansat', 'CANSAT80G2467' => 'cansat', 'CARHR057920' => 'chi', 'CARHR080550' => 'chi', 'CARHR162860' => 'chi', 'Carub.0002s1192' => 'cru', 'Carub.0002s1193' => 'cru', 'Carub.0003s0549' => 'cru', 'Carub.0005s1946' => 'cru', 'Ca_00630_v3' => 'car', 'Ca_08962_v3' => 'car', 'Ca_25544_v3' => 'car', 'Ca_29032_v3' => 'car', 'CBR_g11993' => 'cbr', 'CBR_g23695' => 'cbr', 'CBR_g61495' => 'cbr', 'Cc03_g03290' => 'ccan', 'Cc06_g05140' => 'ccan', 'Cc06_g09990' => 'ccan', 'CDE02G1984' => 'cde', 'CDE02G4074' => 'cde', 'CDE04G0847' => 'cde', 'CDE10G0183' => 'cde', 'Cfa003231' => 'cfa', 'Cfa003247' => 'cfa', 'Cfa009359' => 'cfa', 'Cfa016451' => 'cfa', 'Cfa016528' => 'cfa', 'Cfa021559' => 'cfa', 'Cfa026962' => 'cfa', 'Ciclev10005822m.g' => 'ccl', 'Ciclev10006918m.g' => 'ccl', 'Ciclev10009743m.g' => 'ccl', 'Ciclev10012640m.g' => 'ccl', 'CiPaw.01G161700' => 'cil', 'CiPaw.02G093700' => 'cil', 'CiPaw.04G162000' => 'cil', 'CiPaw.09G008000' => 'cil', 'CiPaw.10G004700' => 'cil', 'ClCG06G005880' => 'cla', 'ClCG06G008790' => 'cla', 'ClCG10G019430' => 'cla', 'COL.COLO4_20848' => 'col', 'COL.COLO4_29825' => 'col', 'COL.COLO4_34817' => 'col', 'Cpa.g.c39921' => 'cpa', 'Cpa.g.sc147.19' => 'cpa', 'Cre01.g014350' => 'cre', 'Cre02.g080900' => 'cre', 'Cre10.g449550' => 'cre', 'CsaV3_1G045760' => 'csa', 'CsaV3_3G036750' => 'csa', 'CsaV3_6G015110' => 'csa', 'CSS0005317' => 'camsi', 'CSS0005328' => 'camsi', 'CSS0008761' => 'camsi', 'CSS0013745' => 'camsi', 'CSS0015457' => 'camsi', 'CSS0028294' => 'camsi', 'CSS0030962' => 'camsi', 'CSS0038829' => 'camsi', 'CSS0049870' => 'camsi', 'DCAR_002310' => 'dca', 'DCAR_012063' => 'dca', 'DCAR_012064' => 'dca', 'DCAR_020783' => 'dca', 'DCAR_027179' => 'dca', 'Dinv19819' => 'din', 'Dinv21266' => 'din', 'Dinv30472' => 'din', 'Dinv36661' => 'din', 'Dinv41628' => 'din', 'Dinv44494' => 'din', 'Duzib093G1714' => 'dzi', 'Duzib106G0212' => 'dzi', 'Duzib150G1142' => 'dzi', 'Duzib151G1052' => 'dzi', 'Duzib160G0385' => 'dzi', 'Duzib168G1113' => 'dzi', 'ECA233G6073' => 'eca', 'ECA234G0450' => 'eca', 'ECA234G3315' => 'eca', 'ECA240G0946' => 'eca', 'EL10Ac7g17003' => 'bvu', 'EL10Ac9g22055' => 'bvu', 'EL10As3g23297' => 'bvu', 'Eucgr.A01555' => 'egr', 'Eucgr.B01112' => 'egr', 'Eucgr.C03812' => 'egr', 'FAN02G0032' => 'fan', 'FAN04G0440' => 'fan', 'FAN05G0567' => 'fan', 'FAN05G5445' => 'fan', 'FAN07G0313' => 'fan', 'FAN07G2278' => 'fan', 'FAN09G4601' => 'fan', 'FAN12G0254' => 'fan', 'FAN14G5507' => 'fan', 'FAN15G2582' => 'fan', 'FAN17G1335' => 'fan', 'FAN19G0909' => 'fan', 'FAN20G1011' => 'fan', 'FAN23G1405' => 'fan', 'FAN26G0904' => 'fan', 'FAN26G1222' => 'fan', 'FAN26G1848' => 'fan', 'FAN26G2783' => 'fan', 'FAN27G0320' => 'fan', 'FAN28G2337' => 'fan', 'FvH4_1g05480' => 'fve', 'FvH4_2g39680' => 'fve', 'FvH4_4g14840' => 'fve', 'FvH4_6g17760' => 'fve', 'Glyma.07G084100' => 'gma', 'Glyma.07G120600' => 'gma', 'Glyma.09G192800' => 'gma', 'Glyma.13G206900' => 'gma', 'Glyma.13G207000' => 'gma', 'Glyma.15G105600' => 'gma', 'Glyma.19G190800' => 'gma', 'Gohir.A01G209900' => 'ghi', 'Gohir.A05G024700' => 'ghi', 'Gohir.A05G132000' => 'ghi', 'Gohir.A08G241900' => 'ghi', 'Gohir.A10G124400' => 'ghi', 'Gohir.D01G198800' => 'ghi', 'Gohir.D05G026200' => 'ghi', 'Gohir.D05G131900' => 'ghi', 'Gohir.D08G262700' => 'ghi', 'Gohir.D10G141900' => 'ghi', 'Gorai.002G243200' => 'gra', 'Gorai.004G280800' => 'gra', 'Gorai.009G026300' => 'gra', 'Gorai.009G135600' => 'gra', 'Gorai.011G158200' => 'gra', 'GSVIVG01015358001' => 'vvi', 'GSVIVG01017908001' => 'vvi', 'GSVIVG01020253001' => 'vvi', 'GSVIVG01026530001' => 'vvi', 'GSVIVG01033769001' => 'vvi', 'HanXRQChr03g0087111' => 'han', 'HanXRQChr08g0228231' => 'han', 'HanXRQChr10g0318701' => 'han', 'HanXRQChr12g0355041' => 'han', 'HanXRQChr12g0359601' => 'han', 'HanXRQChr13g0399961' => 'han', 'Haze_12404' => 'cav', 'Haze_17952' => 'cav', 'Haze_19527' => 'cav', 'Haze_25776' => 'cav', 'Hma1.2p1_0511F.1_g168990' => 'hma', 'Hma1.2p1_1195F.1_g265930' => 'hma', 'HPP92_003558' => 'vpl', 'HPP92_004895' => 'vpl', 'HPP92_011560' => 'vpl', 'HPP92_024580' => 'vpl', 'HPP92_024635' => 'vpl', 'HPP92_024636' => 'vpl', 'Hund06639' => 'sun', 'Lalb_Chr01g0018361' => 'lal', 'Lalb_Chr18g0056191' => 'lal', 'Lalb_Chr20g0112251' => 'lal', 'Lalb_Chr24g0397441' => 'lal', 'Lj1g0019128' => 'lja', 'Lj1P1065T44' => 'lonja', 'Lj1P517T2' => 'lonja', 'Lj1P517T3' => 'lonja', 'Lj2g0015698' => 'lja', 'Lj2P128T31' => 'lonja', 'Lj3A1004T96' => 'lonja', 'Lj6A573T93' => 'lonja', 'Lj6A576T58' => 'lonja', 'Lj6g0011312' => 'lja', 'Lj7A656G58' => 'lonja', 'Lsat_1_v5_gn_2_21441' => 'lsa', 'Lsat_1_v5_gn_5_147260' => 'lsa', 'Lsat_1_v5_gn_5_61801' => 'lsa', 'Lsat_1_v5_gn_5_73880' => 'lsa', 'Lsat_1_v5_gn_6_27001' => 'lsa', 'Manes.03G023500' => 'mes', 'Manes.03G023600' => 'mes', 'Manes.03G182500' => 'mes', 'Manes.09G060644' => 'mes', 'Manes.16G113400' => 'mes', 'Mapoly0023s0016' => 'mpo', 'Mapoly0057s0026' => 'mpo', 'Mapoly0119s0039' => 'mpo', 'Mapoly0147s0023' => 'mpo', 'MBI01_g30865_MAGBIO' => 'mbi', 'MBI11_g04279_MAGBIO' => 'mbi', 'MBI14_g14413_MAGBIO' => 'mbi', 'MCO10G089' => 'mco', 'MD02G1062900' => 'mdo', 'MD10G1081800' => 'mdo', 'MD12G1016500' => 'mdo', 'MD13G1185800' => 'mdo', 'MD14G1014500' => 'mdo', 'MD15G1190700' => 'mdo', 'MD15G1353500' => 'mdo', 'MD16G1186600' => 'mdo', 'Medtr2g022660' => 'mtr', 'Medtr6g087990' => 'mtr', 'Medtr7g103610' => 'mtr', 'MELO3C009429.2' => 'cme', 'MELO3C021410.2' => 'cme', 'MELO3C024691.2' => 'cme', 'Migut.K00498' => 'egut', 'Migut.L01750' => 'egut', 'Migut.N00159' => 'egut', 'MSTRG.10346' => 'ama', 'MSTRG.19574' => 'ama', 'MSTRG.24754' => 'ama', 'MSTRG.26655' => 'ama', 'Nitab4.5_0000132g0220' => 'nta', 'Nitab4.5_0000611g0010' => 'nta', 'Nitab4.5_0000630g0060' => 'nta', 'Nitab4.5_0000968g0010' => 'nta', 'Nitab4.5_0001922g0060' => 'nta', 'Nitab4.5_0002602g0030' => 'nta', 'Nitab4.5_0005504g0020' => 'nta', 'Nitab4.5_0011483g0020' => 'nta', 'Nitab4.5_0021039g0010' => 'nta', 'Nn1g04960' => 'nnu', 'Nn3g18114' => 'nnu', 'Nn4g26226' => 'nnu', 'Nn6g35070' => 'nnu', 'Oeu018441.1' => 'oeu', 'Oeu018713.1' => 'oeu', 'Oeu030325.1' => 'oeu', 'Oeu038892.1' => 'oeu', 'Oeu060217.1' => 'oeu', 'Oeu062811.1' => 'oeu', 'Os01g0266600' => 'osa', 'Os01g0675100' => 'osa', 'Os02g0192700' => 'osa', 'Os06g0625500' => 'osa', 'Peaxi162Scf00110g00183' => 'pax', 'Peaxi162Scf00184g00055' => 'pax', 'Peaxi162Scf00231g00424' => 'pax', 'Peaxi162Scf01196g00023' => 'pax', 'Peaxi162Scf01336g00018' => 'pax', 'PGR004G0235' => 'pgr', 'PGR102G0623' => 'pgr', 'PGR142G2799' => 'pgr', 'PGSC0003DMG400005097' => 'stu', 'PGSC0003DMG400008994' => 'stu', 'PGSC0003DMG400028266' => 'stu', 'PGSC0003DMG401002721' => 'stu', 'Phvul.001G186000' => 'pvu', 'Phvul.004G166100' => 'pvu', 'Phvul.006G151701' => 'pvu', 'Phvul.006G151800' => 'pvu', 'Potri.001G423500' => 'ptr', 'Potri.013G102100' => 'ptr', 'Potri.018G083500' => 'ptr', 'Potri.019G024000' => 'ptr', 'Pp3c11_23160' => 'ppa', 'Pp3c13_7010' => 'ppa', 'Pp3c1_17990' => 'ppa', 'Pp3c2_19280' => 'ppa', 'Pp3c3_490' => 'ppa', 'Pp3c3_500' => 'ppa', 'Pp3c6_3990' => 'ppa', 'PRCOL_00002341' => 'pco', 'PRCOL_00003247' => 'pco', 'Prupe.1G153400' => 'ppe', 'Prupe.1G378100' => 'ppe', 'Prupe.7G118900' => 'ppe', 'Prupe.7G226400' => 'ppe', 'Psat1g044080' => 'psa', 'Psat1g182960' => 'psa', 'Psat3g036000' => 'psa', 'Psat5g124080' => 'psa', 'PSO017G2327' => 'pso', 'PSO170G6057' => 'pso', 'PSO302G0118' => 'pso', 'PSO339G3852' => 'pso', 'PSO339G6162' => 'pso', 'PSO384G1722' => 'pso', 'PSO675G3375' => 'pso', 'QL02p046334' => 'qlo', 'QL06p003739' => 'qlo', 'QL07p040702' => 'qlo', 'RcHm_v2.0_Chr2g0091161' => 'rch', 'RcHm_v2.0_Chr3g0471981' => 'rch', 'RcHm_v2.0_Chr4g0395851' => 'rch', 'RcHm_v2.0_Chr4g0417421' => 'rch', 'RcHm_v2.0_Chr4g0417491' => 'rch', 'RcHm_v2.0_Chr6g0275251' => 'rch', 'RcHm_v2.0_Chr6g0301191' => 'rch', 'Rhsim03G0082000' => 'rsi', 'Rhsim04G0203600' => 'rsi', 'Rhsim08G0224700' => 'rsi', 'Sabra18G0071400' => 'sbr', 'Sabra19G0033900' => 'sbr', 'SalBow3G1013' => 'sbo', 'SalBow5G2912' => 'sbo', 'SalBow5G3279' => 'sbo', 'SalBow6G0779' => 'sbo', 'Sc02g0001180' => 'sci', 'Sc15g0002140' => 'sci', 'Sc19g0004410' => 'sci', 'Sed0017082' => 'sed', 'Sed0023718' => 'sed', 'Sed0024281' => 'sed', 'Sed0027458' => 'sed', 'SEGI_06907' => 'sgi', 'SEGI_07747' => 'sgi', 'SEGI_11073' => 'sgi', 'SEGI_13163' => 'sgi', 'SEGI_14266' => 'sgi', 'SEGI_14919' => 'sgi', 'SEGI_23847' => 'sgi', 'SEGI_26001' => 'sgi', 'SEGI_26015' => 'sgi', 'SEGI_26233' => 'sgi', 'SEGI_29260' => 'sgi', 'SEGI_39591' => 'sgi', 'SGA_v2.0_scaffold11G05936' => 'sas', 'SGA_v2.0_scaffold184G39921' => 'sas', 'SGA_v2.0_scaffold35G14101' => 'sas', 'SGA_v2.0_scaffold35G14103' => 'sas', 'SGA_v2.0_scaffold390G50596' => 'sas', 'SHI26064' => 'shi', 'SMO147G0260' => 'smo', 'SMO151G0005' => 'smo', 'SMO223G0001' => 'smo', 'SMO356G0563' => 'smo', 'SMO367G1092' => 'smo', 'Solyc01g079820.3' => 'sly', 'Solyc07g020860.3' => 'sly', 'Solyc10g083650.1' => 'sly', 'Sopen01g031580' => 'spe', 'Sopen07g008960' => 'spe', 'Sopen10g033120' => 'spe', 'Sp3g05000' => 'spa', 'Sp5g09360' => 'spa', 'Sp5g21040' => 'spa', 'Sp5g21050' => 'spa', 'TAR365G0327' => 'tar', 'TAR365G0931' => 'tar', 'TAR625G0833' => 'tar', 'TAR626G0674' => 'tar', 'TAR633G1376' => 'tar', 'TAR636G0563' => 'tar', 'TAR636G1125' => 'tar', 'TAR636G1529' => 'tar', 'TAR636G2799' => 'tar', 'TAR636G3167' => 'tar', 'TAR636G3377' => 'tar', 'THA.LOC104799074' => 'tha', 'THA.LOC104802755' => 'tha', 'THA.LOC104818807' => 'tha', 'THA.LOC104823470' => 'tha', 'Thecc.04G225000' => 'tca', 'Thecc.05G080200' => 'tca', 'Thecc.06G094300' => 'tca', 'Thecc.09G106600' => 'tca', 'Thhalv10010680m.g' => 'esa', 'Thhalv10019244m.g' => 'esa', 'Thhalv10019251m.g' => 'esa', 'Thhalv10021549m.g' => 'esa', 'TPR.G28356' => 'tpr', 'TPR.G28418' => 'tpr', 'TPR.G33325' => 'tpr', 'TPR.G36364' => 'tpr', 'TPR.G7650' => 'tpr', 'TWI32G0155' => 'twi', 'TWI34G2016' => 'twi', 'TWI36G0390' => 'twi', 'TWI53G0578' => 'twi', 'TWI53G1300' => 'twi', 'unitig_27.g24908' => 'ugi', 'unitig_699.g19025' => 'ugi', 'unitig_749.g13402' => 'ugi', 'unitig_8.g4961' => 'ugi', 'vmacro18879' => 'vma', 'vmacro20726' => 'vma', 'VMungo0464G1876' => 'vmu', 'VMungo0540G1628' => 'vmu', 'VMungo0540G1766' => 'vmu', 'VMungo1383G2071' => 'vmu', 'Zm00001eb059110' => 'zma', 'Zm00001eb128160' => 'zma', 'Zm00001eb303330' => 'zma', 'Zm00001eb360190' => 'zma', 'Zm00001eb387780' => 'zma' ) $gf_id = 'HOM05D001298' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001298' ) $data_identifier = 'HOM05D001298' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 7, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 2, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 12, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb387780' $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